Examples with Taxon dr.evolution.util.Taxon used on opensource projects

Example 6 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class SpeciesTreeStatistic method isCompatible.

private boolean isCompatible(NodeRef popNode, Set<String> species) {
    if (popTree.isExternal(popNode)) {
        Taxon speciesTaxon = (Taxon) popTree.getTaxonAttribute(popNode.getNumber(), "species");
        species.add(speciesTaxon.getId());
    } else {
        Set<String> speciesTaxa = new HashSet<String>();
        int childCount = popTree.getChildCount(popNode);
        for (int i = 0; i < childCount; i++) {
            if (!isCompatible(popTree.getChild(popNode, i), speciesTaxa)) {
                return false;
            }
        }
        if (species != null) {
            species.addAll(speciesTaxa);
            NodeRef speciesNode = TreeUtils.getCommonAncestorNode(speciesTree, speciesTaxa);
            if (popTree.getNodeHeight(popNode) < speciesTree.getNodeHeight(speciesNode)) {
                return false;
            }
        }
    }
    return true;
}

Example 7 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class TestCalibratedYuleModel method createTreeModel.

protected TreeModel createTreeModel(int treeSize) throws Exception {
    taxa = new Taxa();
    for (int i = 0; i < treeSize; i++) {
        taxa.addTaxon(new Taxon("T" + Integer.toString(i)));
    }
    //System.out.println("taxaSubSet_size = " + taxaSubSet.getTaxonCount());
    Parameter popSize = new Parameter.Default(treeSize);
    popSize.setId(ConstantPopulationModelParser.POPULATION_SIZE);
    ConstantPopulationModel startingTree = new ConstantPopulationModel(popSize, Units.Type.YEARS);
    Tree tree = calibration(taxa, startingTree);
    //treeModel
    return new TreeModel(tree);
}

Example 8 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class Utils method taxaToString.

// END: taxonToString
public static String taxaToString(Taxa taxa, boolean printNames) {
    String string = "";
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        string += taxonToString(taxon, printNames) + ("\n");
    }
    return string;
}

Example 9 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class Utils method importTaxaFromFile.

// END: countLines
public static Taxa importTaxaFromFile(File file) throws IOException {
    Taxa taxa = new Taxa();
    Taxon taxon;
    String[] lines = Utils.loadStrings(file.getAbsolutePath());
    for (int i = 0; i < lines.length; i++) {
        String[] line = lines[i].split("\\s+");
        taxon = new Taxon(line[TaxaEditorTableModel.NAME_INDEX]);
        taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, Double.valueOf(line[TaxaEditorTableModel.HEIGHT_INDEX]));
        taxa.addTaxon(taxon);
    }
    return taxa;
}

Example 10 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class Utils method removeTaxaWithAttributeValue.

// END: importTreeFromFile
public static void removeTaxaWithAttributeValue(PartitionDataList dataList, String attribute, String value) {
    for (int i = 0; i < dataList.allTaxa.getTaxonCount(); i++) {
        Taxon taxon = dataList.allTaxa.getTaxon(i);
        if (taxon.getAttribute(attribute).toString().equalsIgnoreCase(value)) {
            dataList.allTaxa.removeTaxon(taxon);
            i--;
        }
    }
}